How to get the nsites parameter that is requiered to run r8s software and then CAFE?

Question

[imda]

Hi there,

I want to run CAFE but I have to produce an ultrametric tree. I am using r8s program. I got the tree from Orthofinder and therefore I have the alignments that were used to get the tree. My problem is that r8s program needs the number of sites in the sequences that were used to estimate the branch lengths (nsites). I do not know how to get this? Can anyone help me?

Answer 1

[Ben Fulton]

The nsites parameter is simply the total number of columns in the alignment(s) used to construct your species tree. Note that for input to r8s, the species tree must have branch lengths in terms of relative number of substitutions (as commonly given from maximum likelihood programs like RAxML. I'm not entirely sure how OrthoFinder does species tree inference, but as long as it uses a multiple-sequence alignment and infers a tree with branch lengths in relative number of substitutions, then you should easily be able to count nsites from the alignment.